If Manaka becomes the new ringleader and share the MC with the other girls, it'll be a win-win ending to all of them because each of them has a feeling for the
MC and previously had individually done it with the
MC without letting the others know.
Now, the whole group is in on it, turning them into a gang consisting of four girls and one slave. They may arrange a weekly schedule for the
MC to serve each girl. LOL
The harem ending will be a smart solution to please all readers who prefer the MC to end up with Manaka, Chisaki, Kanako or Tsubomi because he ends up with all of them. LOL
LOL, sorry being out of the loop as I just discovered on the official web site that Ueno-kun Has Been Developed (Ueno-kun wa Kaihatsuzumi) started as a one-shot before being expanded into a full series, and the Manaka character wasn't in it.
https://yanmaga.jp/viewer/comics/堅忍有抜/
And if we look at the covers of the 8 tankōbon volumes,
Manaka appeared on only 2 volumes while the three girls each featured on 4 volumes! This demonstrates that she is, in fact, a supporting character.
So, @Cross-21-'s analysis is likely correct that the author originally intended Chisaki to be the FMC but the supporting character Manaka's popularity made it inevitable that the story would shift to pair the MC with her instead.
IMHO, if the author is sticking to the one-shot's core narrative, the story really ought to end with a harem. Otherwise, it wouldn't be an expansion of the one-shot into a manga series but rather just a spin-off because readers from the one-shot thought Chisaki was the FMC.